Stargate Atlantis Season 6
by 09jadams
Summary: Atlantis returns to the Pegasus galaxy and finds itself in the middle of a dangerous war between the Genii and the Thorne... Meanwhile, another new enemy enters the Pegasus dimension with plans of invasion! This is how I think Atlantis should have continued if a Sixth series had been made.
1. Ep 1: Hidden Command

**Episode 1: Hidden Command**

Colonel John Sheppard was extremely nervous. He had woken up that morning relaxed and ready for what was coming but now he was in a deep panic. Today was the day that Atlantis would be inspected and scrutinized to decide if it was ready for duty. Since Richard Woolsey had left Atlantis, Colonel Sheppard had been left in charge, which he was particularly good at. But today, for the first time in a very long time, he was nervous. If this inspection went wrong, Atlantis would be taken over by the IOA with the rest of Atlantis booted back to the SGC. This was not a day to make any mistakes.

Sheppard watched out over the beautiful ocean as the waves slowly followed the currents of the water. It was beautiful, almost as beautiful as the seas in the Pegasus galaxy were. Atlantis had been almost immediately moved away from where it had originally landed on Earth to a new location where it would not be found: somewhere in the Pacific Ocean. It meant Atlantis was rarely disturbed, although occasionally it was. On one occasion, a small fishing ship had arrived near the station and the Colonel had been left battling to active the ship cloak so that it would not be found.

The moment of peace Sheppard was enjoying was immediately interfered by Chuck (the gate controller) as he called the Colonel to the gate room. "The guests have arrived, sir." Chuck told the Colonel over the radio. Sheppard reacted as soon as he heard this; he was sprinting down the Atlantis corridors to get to the gate room as fast as he could.

?

General Paul Clark and Dr Liam Johnson stood in the gate room with Chuck, waiting for Colonel Sheppard to arrive. The pair had been given the job of evaluating Atlantis, much to their disliking. General Clark and Dr Johnson were good people and so didn't enjoy pointing at the problems with everything but when a job called, the pair would follow the description. And evaluating Atlantis for the IOA clearly had the description of pointing out everything wrong with what the Colonel was doing. They stood straight, ready to confront the Colonel. Minutes past and the Colonel still hadn't arrived, much to Chuck's disliking. He already had the feeling that this evaluation wasn't going so well.

When the Colonel finally arrived, Chuck to the excuse of dismissing himself. Colonel Sheppard was extremely pleased to discover that his inspectors would be General Clark and Dr Johnson; he had encountered the pair before. In fact, he had even served on a couple of missions with them whilst Atlantis had been on Earth (and Woolsey had been in charge). The General and the Colonel had always got on very well which meant that a great weight had now been lifted off of the Colonel's shoulders. Everything was going to be okay, wasn't it?

"Colonel Sheppard, how are you?" Asked the General. He seemed very pleased to see Sheppard today.  
"Very good, thanks, sir." The Colonel replied in a very unenthusiastic way. As much as Sheppard like General Clark, he didn't want to have this 'stupid' inspection or evaluation as the IOA called it.  
"You don't seem pleased to see us, sir." Dr Johnson said, with a large smile spread across his face. The Dr's smile was contagious and soon the Colonel also found himself smiling.  
"Any way, to the evaluation..." begin the General, "I need to meet your staff before I do anything else. Do you mind introducing us to them?" The Colonel's face lit up when the General said this; the others could deal with this evaluation now...

?

Dr Rodney McKay was worried. His experiment had gone completely wrong and now he had accidentally knocked out Dr Zelenka because of it. He sat by the Dr, shaking him viciously with the hopes of waking him up. "For flip sake," he began, "get up. It was just an accident." When Zelenka did not respond, he suddenly felt terrified. What if Zelenka was dead? What would happen to Rodney? McKay was showered in relied when Zelenka slowly lifted his body off of the ground and looked at him.  
"What did you do?" Zelenka asked. McKay didn't want to answer, which resulted in a moment of silence. This silence was interfered by Zelenka swearing in his Czech Republican language. "What did you do?" Zelenka asked again.  
"I stunned you, that's all. Unless you were pregnant, the stun will have had no physical affect on your body at all." Rodney informed the Doctor. Zelenka was still not that sure on Rodney's explanation.  
"You thought that you'd killed me, didn't you?" This was less of a question and more of a statement. "Didn't you Rodney?" Zelenka was desperate for Dr McKay to respond to him.

The conversation between the pair halted immediately when General Clark and Dr Johnson entered the room, closely followed by Colonel Sheppard. General Clark smiled as he went to shake Dr McKay's hand.  
"Hi, I'm General Clark." The General told him. Dr McKay did not seem amused.  
"Yes, I know who you are." Rodney said, pretending to be bored. He hated inspections and hated being disturbed. The General was both inspecting him and disturbing him at the same time, which left the McKay feeling mad. McKay unhappily accepted the hand shake from the General but did not do so without showing how annoyed he was. Dr Zelenka was more positive about seeing the General and Dr Johnson.  
"Sir, it's an honor to meet you." Zelenka said with a cheeky grin on his face. He wanted to make a good impression. He wanted to make a better impression than Rodney, anyway.

?

Teyla Emmagan and Ronon Dex were sparing. Both of them were skilled fighters which meant that these sparing sessions usually went on for hours on end. They had already been fighting for one hour. Ronon, being a man, was more talented with using his strength but Teyla was far more skilled with her fighting skills. This made both of them an even match in ability. The battle had began with Teyla giving Ronon a strike to the head. This was no normal strike to the head: it was bad enough to knock out most humans. This had affected Ronon's fighting ability slightly but a few strikes to Teyla's waste had made the fight even again.

Now the pair were both tired and injured. They both knew that they would need to go to the medical wing after this but that fact did not stop them from fighting like they had taken no damage. The fought strongly, and as a result stained the room around them with their blood. Ronon took a lucky strike at Teyla, hitting her in the ankle and tripping her over. She screamed in pain as she crashed to the floor.  
"I win." Ronon said, simply. A big smile was spread across his bloody face, even though he was going through immense pain. Winning was extremely important for Ronon; even if it made him feel terrible.

The two were disturbed when General Clark and Dr Johnson entered the room. They seemed to both look annoyed, which made Teyla think that they had already talked to Rodney. She lifted herself onto her feat, ignoring the pain in her ankle, and slowly approached the General. He smiled as he shook her hand; she was allot more positive than Dr McKay had been. Ronon was less positive however. Like McKay, Ronon hated being disturbed unless it was somebody telling him that he was needed to go and kill some Wraith. After some massive encouragement from Teyla, Ronon reluctantly talked to the General. Ronon had known that this would happen today but he had not expected it to be so boring.

?

Dr Rodney McKay sat alone in the cafeteria when Ronon and Teyla entered the room. Both of them looked bored out of their minds which suggested to McKay that they had already been evaluated. He watched as they took up their trays and joined him on his table. McKay's usual look of arrogance stretched across his face. "So I guess you had General So-and-so scrutinizing you?" McKay asked the pair. Ronon and Teyla looked at each other before Teyla decided to talk. Her voice was firm and showed that she was not in the mood to be messed about with.  
"Yes, we did. I didn't find the men to bad to talk to but the questions were... tiring." It was clear that she didn't want to talk about it but Rodney couldn't pick up her hints.  
"They dropped in just after I'd stunned Radek, lucky me! And guess what, they liked him more! Can you believe that?" It was clear that McKay had been desperate to get this out of his system.  
"I don't like them." Ronon said, simply. He wasn't joking, he was just being blunt.  
"No, I like them, I just found them extremely annoying." Teyla told Ronon, in a way which sounded like she was correcting him. There was a moment of silence again before Ronon talked.  
"I don't like them." And with that, Ronon tucked into his food.

The group sat at the table for half an hour, eating the food which sat on their trays. Ronon was finished first; he ate like a wolf which had been deprived of food for the last five years. When he was done, he simply got up and left. That was when McKay noticed how many injuries Ronon had. McKay looked at Teyla before he asked:  
"You been fighting?" Teyla gave McKay an evil stare and so Rodney backed down. She was clearly quite annoyed which meant that when she got up to leave, Rodney felt a bit relieved. Limping away, Teyla vanished from the room, leaving Rodney alone once more. Still hungry, Rodney launched himself to his feat and grabbed himself a new tray of food. "Much better, some piece and quiet." He told himself. Really, he wanted the company but he wasn't very good at showing this. He liked having friends... But he didn't like having friends when they had just been scrutinized by inspectors.

?

Far away, in the Pegasus galaxy, a fleet of massive space ships sat calmly in the middle of the sky. They were gold and bronze; standing like the strongest statues that had ever been made. At first, they were alone, but after time, a new space ship appeared. It was scrap, covered in green and brown, and looked like the sort of thing you would find in a junk yard. The junk ship stopped when it met the other better designed ones and tried to hail it. This resulted in a warning shot from the gold and bronze ships. This other ship wasn't going anywhere near these good ones... Everything was tense, like a fight could start out at any moment.

Inside one of the gold and bronze ship, the Thorne commanders sat ready for war. The Thorne were massive, the size of two men put together, and were a dark brown. Big teeth sat in their mouths and their eyes shone out like the night sky. Each Thorne wore metal Armour, like the sort a knight would wear, but instead the Armour was gold. The Thorne leader, Quantec, sat at the head of the table; preparing to talk to his fellow commanders. He looked firm, ready for war. "Can you confirm that the ship approaching us belongs to the Genii?" Quantec asked his fellow commanders. One of the smaller, weaker commanders looked at a computer panel before he turned back to face Quantec.  
"Yes, it is the Genii." The commander told Quantec.  
"Good. You are to send them a message," he began, "telling them that their development in our space has drove us to the brink of war. If they do not back down, we will have to execute them all!" The commander did exactly as Quantec asked.

Minutes later, the computer screen started flashing red. The weak commander stormed towards the screen to find that a new message had been sent by the Genii. _WE__ WILL NOT BACK DOWN. _That was what the Genii had told them. And so the Thorne ships began fire on the Genii ship, taking down the ship's shield and eventually destroying it. As the scrap pieces of the Genii ship scattered into deep space, the Thorne prepared for their plan to destroy the Genii once and for all. It involved a city, a city which had vanished years ago, it involved Atlantis...

?

Colonel John Sheppard, General Paul Clark and Doctor Liam Johnson were striding down the left wing of Atlantis when the Colonel got a radio call from Chuck. Chuck was clearly in a panic so the Colonel took it upon himself to go and see him. Leaving General Clark and Dr Johnson with Rodney McKay, Colonel Sheppard went to see the gate watcher.

When Sheppard finally reached the gate room, he found Chuck disturbed and nervous. He had clearly been shaking out of fear and it appeared that he had been nervous for quite a while. "Chuck, what's up?" The Colonel asked him. Chuck simply showed the Colonel his laptop screen for Sheppard to understand. The laptop was telling them that 1000 miles away sat a massive space ship. It also sat in the sea, but instead of being in the middle of it, it was right next to the shore. "How long's it been there for?" Colonel Sheppard asked Chuck.  
"Ten minutes," Chuck began, "it's already made itself into the news. The Air force is telling them that the ship is one of theirs but they've already messaged me to say that it isn't." Colonel Sheppard turned to leave but stopped last minute, turning to look at Chuck.  
"I can't leave, I've got visitors," declared the Colonel, "get Major Lorne to assemble a team."

Colonel Sheppard was now running. He had left the inspectors waiting for far too long and he needed them to continue the inspection so that it would finish in time for him to be able to get rid of this strange space ship 1000 miles away. When he finally caught up with the General, he apologized for being late and told them the situation. Not to worried any more, the Colonel, the General and the Dr continued the inspection.

?

Major Lorne had assembled his team and they were now approaching the ship in a cloaked Puddle Jumper. He had bought with him Dr Zelenka, Lieutenant Jessica Haywood and Sergeant William Greel. They were all in the traditional Atlantis battle uniform and all held small P90's. They didn't know what to expect as they approached the ship but knew that being careful was the best option. "Zelenka, where's the best place to park the jumper without being detected?" Lorne asked the Doctor. Lorne was the only one who could fly the Puddle Jumper in his team as he was the only person who had the Ancient gene.  
"I would say that parking the Puddle Jumper on top of the ship would decrease the chances of being picked up by any of the ships scanners. I would think they wouldn't be expecting that." Zelenka told the Major.  
"Okay, I'll park the Jumper on the roof." The Major said.

When Major Lorne finally parked the Jumper, the team explored the roof of the ship; looking for an entrance. Just when they were about to give up hope of finding it, they checked under a random metal panel and found it. Lowering themselves through the entrance, they found themselves in a large golden corridor. It looked very similar to the corridors you would find in a Goa'uld ship. Slowly the team delved deeper into the ship yet they still hadn't come across any aliens yet. A panel on one of the doors confirmed the name of the aliens who owned this ship: the Thorne. They must have been massive because the corridors were! It was just strange that there was no Thorne in this ship.

After a long time of exploration, Zelenka was able to find signs of technology... but he didn't like what he saw. He saw a picture of Atlantis being sent to another Thorne ship! Zelenka began to study the picture and the more he found out, the more disturbed he became. This Thorne ship had been sent to the sea to take control of Atlantis and now the control was being passed onto a more powerful ship! The Thorne had to be stopped before it was too late... If they got away with this, Atlantis could be used as a weapon against the Earth.

Zelenka told the Major about this and the team launched themselves towards the Puddle Jumper. Once inside, the Major flew the Puddle Jumper blast distance away from the Thorne ship. They then began to litter the ship with massive drones. The drones dropped like rocks in water; they had a massive amount of success when they hit the ship. The ship was launched into the sky and engulfed in flames. People who stood by the shore were shocked by the sight and terrified as well. They had been told that this ship was an air force ship so they were convinced that this ship had been destroyed by a terrorist attack. The Air force did nothing to change this view.

Major Lorne was too late, any way... The control of Atlantis had already been handed to a much more powerful ship in the Pegasus galaxy. There was nothing that Major Lorne and his team could do about, Atlantis was out of his control!

?

General Clark was shocked when Atlantis began its flight. Everybody was shocked when Atlantis began its flight. Dr McKay said that some unknown force was dragging Atlantis into the sky and their was nothing that him or anybody could do about it. As Atlantis left the Earth, everybody realized that there was no solution. There was no way to fight this, there was no way to survive. This was the end, for everybody.

Atlantis left the beautiful ocean which had surrounded it with a burst of bright light and powerful energy, resulting in the sea being slightly unsettled. The waves which crashed into the shore that day were bigger than what had been expected. The news said that this was a sign of change, and it definitely was _for _everyone.

**To Be Continued...**


	2. Ep 2: Behind Enemy Lines

**Episode 2: Behind Enemy Lines**

**Part 2 of Hidden Command**

**Previously on Stargate Atlantis:**

Colonel Sheppard, now the leader of Atlantis, had to dead with inspections being led by General Paul Clark and Doctor Liam Johnson. Meanwhile, aliens known as the Thorne declared war with the Genii and planned to use Atlantis as a weapon against them. They landed one of their ships next to Atlantis to take control of the station. Major Lorne and his team attempted to stop the Thorne from taking control but were too late... The control was passed to a much more powerful Thorne ship and Atlantis was raised into the air.

**And now, the thrilling conclusion to ****_Hidden Command: _**

Dr Rodney McKay was shocked. After leaving General Clark and Dr Johnson with Colonel Sheppard once more, he had returned to his research. Looking for a cure for cancer was an extremely important job and so being disturbed by Atlantis launching itself into the sky was extremely annoying. Leaving his laptop behind, Rodney left the lab to try and find Colonel Sheppard. He strode through long black corridors filled with screaming civilians before he finally arrived at Colonel Sheppard's office. Without knocking, Rodney launched himself into the small but comfortable room. "What the heck is going on?" Rodney asked Sheppard.  
"That's exactly what I want to know." General Clark told Rodney. Clark and Johnson stood by Sheppard's desk, confused and demanding questions. This was not what they had had in mind when they had been asked to be inspectors of Atlantis.  
"Look, if you want answers, ask Rodney!" Sheppard screamed. The room turned silent before Sheppard turned to look at McKay. "Right, that's better. Now Rodney, tell us what's happened?"

McKay could give no answer. It just didn't make sense. Spaceships just didn't fly into space by them selves. Atlantis must have been under control by somebody or something. Rodney dismissed himself immediately and returned himself to his lab. There he began to run simulations on his laptop, each showing possible ways for this to have happened. They didn't help, however, as none of the results of the simulations ended in the situation Atlantis was in. Atlantis must have been put under control by somebody, and Rodney wanted to find out. He began to look through the records of recent missions and found the answer straight away... The last mission an Atlantis team had gone on was exploring the space ship which had landed next door to Atlantis. That ship must have taken control of Atlantis and Major Lorne, who had led that mission, must have failed...

?

Major Lorne had not been able to catch up with Atlantis in the Puddle Jumper. Atlantis had smashed its way into the sky so fast that Major Lorne had lost sight of it after only half a second. Him and his team had now returned back to SGC with the hopes of explaining what had happened. There he was met by General Samantha Carter, who was the leader of the SGC. Confused on where Atlantis had gone she asked: "Where's Atlantis, Major?" Major Lorne had just left his Puddle Jumper and appeared to be extremely tired. He looked at Carter, a large frown spread across his face.  
"Some aliens called the Thorne took it." The Major told her. Carter looked shocked.  
"Say that again?" She asked, almost sarcastically.  
"We tried to stop them but it was too late, they passed the control to another ship before we could destroy them." Lorne told her, panic in his voice. It was clear that he felt like he had let Atlantis down.  
"Is that what that spaceship by the sea shore was for?" Sam asked.  
"Yep, for taking control of Atlantis." Lorne replied.

Sam launched herself out of the room and headed towards the gate room. Walter was sitting on his chair, relaxed and undisturbed. In fact, he was even reading a book. Sam pushed the book out of his hand in disgust.  
"Walter, don't read on duty!" She shouted. Walter gave her an apologetic wave. "I need you to try and dial the Atlantis gate." She asked. Walter did as she demanded but could not reach the Atlantis gate.  
"I can't dial in." Walter told Sam.  
"Thanks for the help." Sam said, whilst she walked away. You couldn't dial a gate if it was moving which meant that what Lorne had just told her must have been the truth. Atlantis was in flight at this very moment, heading to who knew where... All she knew was that she needed to find them before too much damage was done!

?

Atlantis had arrived in the Pegasus galaxy, much to the surprise of Colonel Sheppard. He hadn't expected Atlantis to jump out of Hyperspace so soon so when he discovered that they were in the Pegasus galaxy. Ronon Dex and Teyla Emmagan were one of the first people to find out about this. Teyla was extremely excited; she could finally see her son again. Ronon was also excited; he would get the chance to kill some Wraith again. Ronon and Teyla saw this as a good thing, even though Atlantis was still under the control of something.

Dr McKay thought that he may have answers... A strange ship had been sighted next to Atlantis when it had emerged into the Pegasus galaxy, one very similar to the one at Earth. McKay had to tell Sheppard. He was now running towards Sheppard's office once more, desperate to tell Sheppard of his find. People still stood in the corridors shocked, but this time they weren't crying or screaming, they just seemed a tiny bit shocked. Rodney gave a reassuring smile to his girlfriend, Jennifer Keller, who was now looking after the people who had been injured by the unexpected flight. Keller returned the smile back, which made Rodney feel a bit better.

"It's that ship which was on Earth which caused this!" Rodney proclaimed when he reached Colonel Sheppard's office.  
"Yes Rodney, I already realized that." Sheppard told McKay. McKay looked slightly embarrassed by this.  
"Well anyway, one of those ships is right next to us." McKay told Sheppard in a matter-of-fact sort of manner. Sheppard's reaction was extremely unexpected. He launched out of his chair and activated his radio which connected to Chuck.  
"Chuck," he began, "I need you to try and connect my radio to the ship next to us." McKay's reaction to what Sheppard had just said was more expected. He gave Sheppard the evils before he finally left the room.

?

General Clark and Dr Johnson were sitting in the cafeteria together. Today had been surprisingly strange and terrifying; the pair would have been perfectly fine if they had known what they were walking into but they didn't so they weren't fine. They were tired and just wanted to go home. Telling jokes was the only way they could think of for wasting time. "So a cat walks into a bar and says..." Dr Johnson began before being interfered by Colonel Sheppard, who had now entered the room. Sheppard immediately turned to talk to the General.  
"Sir, we've decided to engage with the enemy." Sheppard told him. The General's reaction was of shock and anger. He launched up onto his feat and starred the Colonel in the eyes.  
"As the highest ranking officer in this base, I am demanding that you do not contact them." The General said. There was an unspoken authority which surrounded him.  
"With all due respect, sir, you'd be making a massive mistake to undermine my orders." Colonel Sheppard said. He was clearly unhappy with the General; he didn't like being undermined by anybody _not _even people who were above him.  
"You're planning to make contact with the enemy and give away our location. There's nothing good about this situation!" General Clark was clear; he felt like the boss now.  
"Listen to him, Colonel," began Dr Johnson, "we're safe at the moment."  
"That's the thing, we're not! These aliens put us here, so they're going to know where we are." There was a moment of silence as the three men thought the situation over. "I'm going to talk to these aliens whether you like it or not."

Colonel Sheppard stormed through Atlantis, clearly not happy to have just had that confrontation with the General and the Doctor. He thought that it had been completely unprofessional for the General to undermine him, even if the General was his boss. When he finally reached his office, Chuck had already connected the Colonel's radio to the alien space ship. Plonking himself down on his sofa chair, Colonel Sheppard activated his radio. There was a moment of silence, like the aliens hadn't prepared for this before they said:  
"We are the Thorne." They waited for Colonel Sheppard to respond.  
"Lets forget the introduction. You took control of Atlantis for what reason?" Sheppard was clearly not amused, which left the Thorne feeling a small sense of panic.  
"That is none of your business." Came the reply from the Thorne commander. "Why do you believe that it is your business?"  
"Well, let's see... I run Atlantis and you took control of the damn thing! You had no right!" Sheppard was now belting his words down the radio. Chuck was so shocked that he even entered the office to make sure that the Colonel was okay.  
"We have a right to defend ourselves." The Thorne commander said.  
"Defend yourself from who?" Sheppard asked, slightly interested.  
"The enemy."  
"Who are...?"  
"The Genii!" Declared the Thorne commander.

?

Ronon and Teyla were sparing again when Colonel Sheppard went to find them. After talking to the Thorne, he had established that the Genii had entered Thorne space and the Thorne wanted to use Atlantis as a weapon against the Genii. However, using Atlantis meant that many innocent planets would be destroyed in the process. So Colonel Sheppard had offered another solution... He would visit the main Genii fleet, force them to leave the Thorne part of space and get to take control of Atlantis again. All he needed to do was assemble his team.

The Colonel eventually found Ronon and Teyla; giving them the mission briefings. Rodney McKay was easy to find: he was in his lab like he always was. Once the team was assembled, Sheppard went to find the General. He didn't want to leave the General on bad terms and so left the General as commander over Atlantis. The team geared up and got into the Puddle Jumper. There, Colonel Sheppard began the long flight into space. General Clark watched them go, slightly nervous about what was about to happen. "They'll be fine," Johnson reassured him, "they always are!"

It didn't take long for McKay to be able to locate the Genii main ship and in no time, the Puddle Jumper had approached it. The ship was massive, covered in green and brown, but had clearly been the victim of many space battles (probably with the Thorne). The Thorne part of space was also filled with a few Wraith hives, which meant that getting to the ship would mean avoiding these ships. Luckily, they didn't have to avoid the Wraith when the Genii ship attacked the Hives. The Genii weapons blasted out crystal blue laser beams and in a matter of seconds, the Wraith Hives were destroyed. These Genii were powerful, very powerful.

?

General Samantha Carter was standing in the meeting room with Major Lorne, Doctor Daniel Jackson, Colonel Cameron Mitchell, General Jack O'Neil and Teal'c. She was briefing them on her theory on how the Thorne had known Atlantis was on Earth. The meeting began the moment Jack O'Neil entered the room, as he was very late after a meeting with the Senator. "As you know," Sam begun, "this morning an alien known as the Thorne took Atlantis from Earth and sent it sky high."  
"Yes, I do know, I was there." Lorne said, trying to be funny. This resulted in everybody else in the room giving him evils. "Sorry." He said, his smile now wiped completely off of his face.  
"Any way, the Thorne must have been told by somebody that Atlantis existed, somebody who is against the Genii..." Sam began.  
"Are you thinking what I'm thinking?" O'Neil asked her.  
"It's the Trust." They said together.

The Trust were a movement on Earth who thought they did the jobs which needed to be done but would never be done. This meant that they often appeared as enemies of the SGC, even though they had the same aims. The idea of destroying the threat of the Genii was something which fitted with the Trust regime but some things didn't add up. Why would the Trust want to destroy an evil enemy by helping an evil enemy? It just made no sense. Carter was desperate to find out. Again, she sent Lorne and his team on a new mission...

Since the death of the last Ba'al clone, the Trust had been in hiding. Their attempts to join the Lucian Alliance had gone terribly and resulted in them now using corrupt government officials to cover them up. One of these officials was Randell Shortleg. The SGC had tried to use him to overpower the Trust using Randell many times but could never convince him that the Trust were doing anything wrong. Major Lorne simply had to try and visit Mr Shortleg. If Shortleg was still alive, chances were the officials still protected the Trust and the Thorne wouldn't have been able to infiltrate them. If Shortleg was dead, there would be a small possibility that the Trust had been taken over by the Thorne.

When the Major and his team arrived at Shortleg's house, they had to force their way through the door. There they found the rotting dead body of Mr Randell Shortleg. It appeared that he had been dead for months but for some reason, nobody had found him... Maybe the Thorne had taken over the Trust? That would explain how they knew about Atlantis...

?

Colonel Sheppard and his team had now crept into the Genii ship without being detected. Striding down a long green corridor, the team soon came across a small brown room. The room was filled with different control panels, all show the main locations of the ship. McKay stopped by one of the panels and began to evaluate them. "We need to get to this room here," he said whilst pointing at a small docking location at the end of the ship. "If I can get to one of the computers in that room then I can program the ships to naturally leave the Thorne part of space. Returning will simply destroy the Hyper-drives." Rodney told the Colonel.  
"How many men would we have to take out to get there?" Sheppard asked.  
"I don't know! Maybe a hundred." Rodney answered.  
"One hundred? Don't you think that will be just slightly too dangerous?" Sheppard said, not asking a question; stating a fact.  
"I can handle 'em." Ronon told the Colonel in a simple but aggressive way. "If I can kill a hundred Wraith with my bare hands, I can kill a hundred Genii with a gun."

The team stormed forwards down the corridor, firing with great aim at the enemy which were approaching them. Ronon took the lead in taking out enemies; Sheppard and Teyla took out any of Ronon's survivors. When they finally reached the last corridor, they were shocked by what they saw! 30 Genii stood in the corridor, ready for battle. One man, who appeared to be their leader, stepped forwards.  
"Colonel Sheppard, I've been expecting you." Nobody expected Ronon to launch up his gun and shoot the leader in the leg. The leader collapsed to the floor in pain, his men around him now firing at Sheppard and the team.  
"Ronon, what have you done?" The Colonel asked whilst shooting his gun at the enemy.

The team continued to fight, desperate to not lose a man. All of them made good shots. Teyla was able to take out three men at once by taking a close up head shot at a man on the front line. McKay and Sheppard were able to take down some of the men at the back. Ronon was able to take down most of the men any way. In fact, you could even say that Ronon would have won the fight without the rest of the team. Once the battle was over, McKay launched himself into the docking room and to the control panel. He quickly changed the ship location drive to be out of the Thorne space before the team left to leave.

Getting back to the Puddle Jumper was easy, only a few Genii got in the way of the team and they were all easily defeated. Once the team was inside the Jumper, Sheppard flew the ship to safety. Their they watched the Genii ships slip away out of Thorne space back to where it had started: elsewhere. The team had won, the Genii had been defeated.

?

The Thorne kept their promise and gave the power of Atlantis back to Colonel Sheppard, which meant that Atlantis was now controlled by Earth again. The team were able to fly Atlantis to a planet with a large ocean. SGC were massively relieved when they were able to get contact with Atlantis again. General Paul Clark and Dr Liam Johnson returned back to Earth, also relieved...

But it wasn't over yet! The Thorne still controlled the Trust on Earth. The Genii and the Thorne were still at each others throats. The end was far away, and it would take a while to reach it. And while SGC celebrated contact with Atlantis again, the Genii counted their losses. When they eventually found their injured leader, the pledged war against Atlantis. Everybody would fall into the hands of the Genii!

**The End...?**

**Written by J.W.D Adams. **


	3. Ep 3: Wraith of Mine

**Episode 3: Wraith Of Mine**

**Previously on Stargate Atlantis:**

Major Lorne returned to SGC to tell them about the Thorne situation. They were able to discover that the Trust was being run by the Thorne 'through' a man called Shortleg. Meanwhile, Atlantis agreed to take down the Genii force if they were given full control over Atlantis again. Doctor Rodney McKay was able to hack into the Genii system so that the Genii ships left Thorne space. Now the Genii leader wants revenge on Atlantis and the Trust has begun to fall apart...

**And now, the Genii see a new solution...**

Robert Kindle, a government official, wasn't alone; even though he wanted to be... He sat on he chair in his upstairs bedroom whilst his personal body guards who worked for the Trust protected him down stairs. He wished he'd never got involved with them, after what had happened to Mr Shortleg. If he'd never got involved, he may have been safe right now but instead: he was one of the most wanted men on this world! After the Trust's new owners had been revealed, SGC had been even more desperate to bust up the Trust as taking down the Trust meant taking down the Thorne. Any minute now, an SGC team would turn up, destroy everything the Trust had started through Robert and leave him as a simple corpse!

Minutes later, as Robert had predicted, SG: 1 launched through his front door. Each of them were heavily armed and ready for battle. The Trust men tried to fight back but were out skilled. Robert sat in fear as he heard SG: 1 destroying his legacy, his future. Hatred drenched his lungs as his men collapsed to become one with the Earth. Knowing his moment was coming, Robert decided not to deal with the pain of being interrogated and tortured by the SGC. He simply lifted his gun to his head and fired. Blood splattered the floor, leaving stains which would mark them forever. When SG: 1 finally reached Robert's door, they were devastated to find Robert already dead. SGC had been using corrupted government officials to track down the next Trust member and now Robert was dead, they could do no more. It was all up to Atlantis now...

The only way for them to take down the Trust would be to find a new list of officials in the Thorne data base, and that would be very, very hard even for the Atlantis team.

?

"Look, Colonel, Earth's demanding to see you." Chuck told Colonel Sheppard, trying to clear the Colonel's head.  
"Chuck, I've had a busy day, tell them that I'll come another time." The Colonel asked Chuck, although his intentions were clear.  
"Sir, they demand it." There was a moment of pause whilst Sheppard decided what to do next. After a few seconds he said:  
"Fine, tell them I'll be there in a minute."  
"Sir, they asked you to bring a suit case." Chuck told Sheppard. Sheppard looked a bit stunned but just decided to do as Chuck had been told. He left the room to head to his quarters.

Sheppard packed everything he thought he would need: Official uniform, guns, his phone and a radio. After doing this, he launched his travel bag onto his back and headed towards the gate room. Chuck had already activated the Stargate for the Colonel; it was connected to Earth as expected. Sheppard gave Atlantis a quick wave to say goodbye before he entered the gate ready for whatever would happen next. There was something about going through the gate which made you excited every time. It was like going on a roller coaster for the first time in your whole life. Sheppard loved it.

As the blur of the wormhole slowly faded away, Sheppard found himself in the SGC. General Carter was already there to meet him and after saying their hellos, they headed off to Carter's office. In the office sat four different people: Colonel Mitchell, Doctor Daniel Jackson, Teal'c and General Clark. Sheppard was shocked, he had only expected to have a chat with Carter.  
"Colonel, please sit down." Carter asked in a friendly manner. Sheppard sat himself onto a stray chair and prepared for what was to come next. "First of all, good news! We've finally found a replacement." Sheppard had been properly surprised now.  
"You did what?" He asked her.  
"John, you must have known you were never going to be the permanent expedition leader." Carter spoke, in a way which was clearly not a question. Colonel Sheppard couldn't hide his surprise and disappointment.  
"Who's my replacement?" Sheppard asked. General Clark was the next person to speak.  
"I am," he said, "sorry Colonel!"

?

For some stupid reason, Sheppard had left Dr Rodney McKay in charge of Atlantis whilst he visited Earth. Maybe it was because McKay would make a good leader or more likely, maybe it was because Sheppard didn't think he would be gone for long? Who knew? But McKay was in charge, and whilst he was, he was making sure that everything he had dreamed of doing to Atlantis was being done. He had even accidentally wiped out the electricity just trying to make the tap water cooler.

McKay was also the first person to pick up on the Genii ships which were heading towards Atlantis... There were dozens of them, maybe even hundreds. Each individually painted in the most terrible way. At first, the only way the ships had been seen was by the scanners but the closer the ships got (which happened by the minute) the more visible they became. Rodney was in panic; he was prepared for war and ready for battle. He had already sent both Teyla and Ronon to the left and right sides of Atlantis in preparation for the battle to come. Major Evan Lorne had been left to look after the other two sides of the city. Strangely, McKay seemed unexpectedly organised.

"Chuck, dial Earth and let the know what's going on." McKay demanded. Chuck began to dial in the Earth address but when he got midway, the Stargate shut down. "Oh not good, not good." McKay said. He snatched Chuck's laptop and gave it a quick study. This wasn't good, this wasn't good at all. "The Genii have blocked the gate! It looks like they really want to get revenge on us for kicking them out of the Thorne galaxy." McKay turned to Chuck in a panic. "Order Ronon and Teyla to begin firing at the ships." Chuck did as McKay had asked.

?

Somebody had dialed the Earth gate; disturbing the meeting which had begun in General Carter's office."Unexpected gate activation!" Walter bellowed at the top of his voice. General Carter, General Clark and Colonel Sheppard were then first to react to what Walter said, and were in the gate room almost immediately.  
"Activate the iris." She demanded, clearly quite nervous.  
"There's no IDC." Walter told General Carter. Carter looked very worried now.  
"Get a team ready outside of the gate, in case of an emergency." General Clark asked Walter. Walter tapped onto his radio and ordered the gathering of SG: 2. Teal'c had now left the meeting room and had joined the group which gave the Colonel and idea.  
"General Carter," he began, "me and Teal'c will go down their and join them!"

Sheppard and Teal'c geared up as quickly as possible and launched themselves into the gate room. Guns in hands, they prepared for what was to come next... They waited and waited and waited for something to happen but nothing dead. Nobody tried to go through the gate. It just remained open; unused and in a way, useless. But then things changed... The enemies sent a sentence through the gate: THE GENII DESTROY ATLANTIS!

?

Teyla stood by the Atlantis laser canon, ready for battle against the Genii which were approaching them. Two soldiers, Sergeant Greel and Lieutenant Haywood, were with her; also standing by canons. It was Teyla's job to decide when it was the right time to begin firing against the enemy. The nearer they got, the more nervous she got... And then she made the decision! Teyla began to open fire at the Genii ships, as did Greel and Haywood. Beams of energy smashed into the side of one of the smaller ships, causing a large explosion.

Ronon had picked up the hints that the battle had started and was now firing with the laser canons himself. Atlantis were doing well, they had already taken down two ships. However, when one of the main ships fired a stray bullet at Ronon, his laser canon was destroyed. Bursting into flames, the canon slowly turned into ashes. Ronon tried to avoid the flames; but it spread so quickly that doing this wasn't going to be that easy. He only just got inside the Atlantis buildings in time.

Teyla was horrified to see Greel be struck by a Genii laser beam! She had to leave her own post to try and help him which meant that Haywood was fighting alone. After a few accurate Genii strikes, Haywood found her laser canon eliminated. Grabbing Greel, Teyla and Haywood launched themselves inside; hoping that they had done enough to give Atlantis a chance of winning.

Nobody outside of the Atlantis command tower had knew what had just happened inside it... Whilst the battle had commenced, a lucky strike had hit the tower and directly planted itself on Chuck. His body had immediately turned to dust; as had his clothes. This was a sign for McKay: this attack was serious. He was just about to give up when he had received a call from the Genii. What they said was simple, but extremely dangerous... "Bring us the Wraith you call Todd," was what they asked, "or we will destroy Atlantis!"

?

"They killed Chuck! They're pretty serious about this!" Rodney screamed at Teyla, who had told McKay that giving Todd over to the Genii would be stupid. Todd had remained in an Atlantis shell since the ship had been taken to Earth. Over time, he had been growing hungrier and hungrier; the urge for feeding above anything else.  
"Rodney, listen to me. They've come here for a purpose which means that if we don't give them Todd, they won't destroy Atlantis. The fact that they came here shows they need him too much to lose him." Teyla told McKay.  
"We should just shoot him." Ronon said. Everybody ignored him.  
"How do we know that they're not going to kill us after we've given them Todd?" McKay's girlfriend, Jennifer Keller, added. This thought suddenly popped into McKay's mind and made him even more uncertain about what to do.  
"I say we shoot him and the Genii." Ronon said, again. But this time everybody listened to him, even McKay.  
"That might just work..." McKay said, thinking out loud.  
"What might just work?" Ronon asked in a puzzled voice.  
"If we implant a bomb and a camera in Todd, we can find out why the Genii need Todd and then destroy them. We could even use Todd to distract them so we can get all of their information about the Thorne!" McKay told the others. "Jennifer, get Lieutenant Haywood and Lieutenant Wakeling to bring you Todd and then implant a camera and bomb inside of him. I need that done in 10 minutes, before the Genii get suspicious." Keller left the room to do as McKay had asked her to do.  
"See, Rodney, giving up isn't always the way." Teyla told the Doctor.  
"Hm, I guess not." Rodney said, clearly proud of himself.

?

Todd was starving. Not being fed for months had left him weak and desperate which meant that the sight of somebody different gave him hope; maybe they were here to put him out of his misery. "Ah, finally my call to die!" Todd said with a forced smile on his face. One of the soldiers, Lieutenant Wakeling, approached Todd, gave him a big strike round the head and shouted:  
"I could kill you right now, don't play games with me!"  
"Kill me then." Todd half joked-half begged. There was a moment of silence before Todd wrecked it with his ridiculous laughing. "I heard the battle going out side, I guess you need my help."  
"Quite the opposite," began Wakeling, "it appears that it's you that bought these people here." Todd was amused; he'd always loved causing trouble but this seemed to top them all as he didn't even know what he had done.

Dr Keller took longer than expected to put the bomb and camera into Todd. Connecting the camera to Todd's vision took exactly half an hour, which caused Atlantis to become the victim of a few Genii warning shots. When the operation was finally done, Todd was left to be beamed up by a Genii mother ship. There he was immediately confronted by Genii soldiers, led by one called Laton. Laton was the commander who had been shot in the leg by Ronon in the mission which resulted in the Genii getting kicked out of Thorne space. Now slowly healing, he was desperate for revenge on Atlantis; even though he was immobilized by dodgy crutches.

Todd was led into a dark room and immediately chained by Laton's men to a metal chair; it appeared that Laton still saw Todd as a threat. Laton felt safer with Todd in chains and slowly started to relax around him.  
"Do you remember the last time the Genii captured you, Mr Todd?" Laton asked the Wraith, desperate for a reaction. There was a moment of pause as the Wraith considered what to say next.  
"Yes." That was all that Todd could say, saying anything else would bring back the horrible memories.  
"Then... you will no what we can do when you don't do as we ask of you." Laton said as simple as possible, with a large smirk across his face.  
"What do you want?" Todd asked, the urge to know deep inside him.  
"Your rewards will be..."  
"What do you want?" Todd was interested; it was clear that he wanted to get back at Atlantis after them keeping him in containment for so long. Revenge was flowing through him.  
"We need the Earth Address."  
"Oh, very interesting!" Todd said whilst laughing.  
"You may or may not know that the Genii are at the brink of war with the Thorne, and we want to win that war before it starts. The majority of the Thorne power is held on an organisation they call the Trust, which is run on Earth. If we can activate the Earth gate and fire a powerful enough beam through the gate, it WILL destroy the Earth and thus take out the Trust. This could be the best way of eliminating..." Nobody got to hear the next sentence.

McKay had finally downloaded the list of Trust members and had now blown Todd sky high. The Genii ship collapsed around him, and those flames took out the others. This had been a massive success for Atlantis. Not only had the finally gotten rid of Todd, they had taken out a massive Genii fleet and found a whole new list of known Trust agents. The future looked bright...

?

After the Genii fleets were destroyed, the Earth gate was mysteriously shut down. Earth dialed in Atlantis the moment after and were relieved to realize that Atlantis had not been destroyed by the Genii. Weeks passed as Sheppard went through the meetings he had meant to go through when he had originally called to Earth. It turned out Carter had wanted Sheppard to lead an investigation into Robert's personal life to try and find contacts to the Trust. After McKay had gained his massive list from the Genii database, Sheppard's mission had changed. He had spent these weeks on Earth leading all of the behind the scenes work on gaining permission to take out these Trust contacts. Slowly, things began to get better. General Clark had gone to Atlantis two weeks before the Colonel had, which meant that he had now fully enforced his control on the place. After time, Atlantis felt the need to have the Colonel once more, and so Sheppard prepared to leave Atlantis.

John Sheppard now stood by the Earth gate in SGC, ready to return home. Carter was there by the gate to say good bye, but really there was something else she wanted to talk about... "Colonel, the message we got..."  
"I know. It's can't be the Genii as they were aiming to get the gate address, so who was it?" Sheppard asked her, although he didn't expect to get an answer in any way at all.  
"John, I want you to make it your priority from now on to find out who sent us that message." General Carter demanded. She seemed extremely worried by what had happened, and definitely wanted it resolved.  
"I find out General, I promise." He told her. And with that he entered the gate and returned to the one place he now sore as home: Atlantis.

**The End...?**

**An upcoming fan-fiction from me will hopefully be airing. It is my version of SG: 1 Season 11 and the main story arc will be taking down the Trust so that the Thorne can be defeated. This means the Trust arc will become more of a background story in Atlantis from now on, unless the other story does not air.**

**Written by Jacob Adams**

Please review as it will encourage me to continue writing and help me to know how to improve my writing and the stories in general. 


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